Highly read on genomebiology.com in April
RNA transcripts can be sequenced from biological samples, but making sense of those that fail to map exactly to a reference genome is tough. Eric Rivals at the University of Montpellier, France, and his team have written a program called CRAC that can identify tricky transcripts as experimental errors, chromosome rearrangements, small mutations or modifications to messenger RNA. The software simultaneously matches discrete portions of sequenced RNA to locations in the genome and counts up how often unique portions are sequenced — a strategy that combines several computational steps. Although CRAC requires more memory than some similar software, it is more sensitive and precise than other tools for classifying RNA transcripts, the authors say.